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Revision 1625 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
Revision 2008 by tim, Sun Feb 13 19:10:25 2005 UTC

# Line 1 | Line 1
1 + /*
2 + * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 + *
4 + * The University of Notre Dame grants you ("Licensee") a
5 + * non-exclusive, royalty free, license to use, modify and
6 + * redistribute this software in source and binary code form, provided
7 + * that the following conditions are met:
8 + *
9 + * 1. Acknowledgement of the program authors must be made in any
10 + *    publication of scientific results based in part on use of the
11 + *    program.  An acceptable form of acknowledgement is citation of
12 + *    the article in which the program was described (Matthew
13 + *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 + *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 + *    Parallel Simulation Engine for Molecular Dynamics,"
16 + *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 + *
18 + * 2. Redistributions of source code must retain the above copyright
19 + *    notice, this list of conditions and the following disclaimer.
20 + *
21 + * 3. Redistributions in binary form must reproduce the above copyright
22 + *    notice, this list of conditions and the following disclaimer in the
23 + *    documentation and/or other materials provided with the
24 + *    distribution.
25 + *
26 + * This software is provided "AS IS," without a warranty of any
27 + * kind. All express or implied conditions, representations and
28 + * warranties, including any implied warranty of merchantability,
29 + * fitness for a particular purpose or non-infringement, are hereby
30 + * excluded.  The University of Notre Dame and its licensors shall not
31 + * be liable for any damages suffered by licensee as a result of
32 + * using, modifying or distributing the software or its
33 + * derivatives. In no event will the University of Notre Dame or its
34 + * licensors be liable for any lost revenue, profit or data, or for
35 + * direct, indirect, special, consequential, incidental or punitive
36 + * damages, however caused and regardless of the theory of liability,
37 + * arising out of the use of or inability to use software, even if the
38 + * University of Notre Dame has been advised of the possibility of
39 + * such damages.
40 + */
41 + #include "selection/SelectionManager.hpp"
42   #include "visitors/OtherVisitor.hpp"
43   #include "primitives/DirectionalAtom.hpp"
44   #include "primitives/RigidBody.hpp"
45   #include "primitives/Molecule.hpp"
46   #include "brains/SimInfo.hpp"
6 –
47   namespace oopse {
48  
49   //----------------------------------------------------------------------------//
50 < void IgnoreVisitor::visit(Atom* atom){
51 <  if(isIgnoreType(atom->getType()))
52 <    internalVisit(atom);
50 > void IgnoreVisitor::visit(Atom *atom) {
51 >    if (isIgnoreType(atom->getType()))
52 >        internalVisit(atom);
53   }
54  
55 < void IgnoreVisitor::visit(DirectionalAtom* datom){
56 <  if(isIgnoreType(datom->getType()))
57 <    internalVisit(datom);
55 > void IgnoreVisitor::visit(DirectionalAtom *datom) {
56 >    if (isIgnoreType(datom->getType()))
57 >        internalVisit(datom);
58   }
59  
60 < void IgnoreVisitor::visit(RigidBody* rb){
61 <  vector<Atom*> myAtoms;
62 <  vector<Atom*>::iterator atomIter;
63 <  AtomInfo* atomInfo;
24 <  
25 <  if(isIgnoreType(rb->getType())){
26 <    
27 <    internalVisit(rb);
60 > void IgnoreVisitor::visit(RigidBody *rb) {
61 >    std::vector<Atom *>           myAtoms;
62 >    std::vector<Atom *>::iterator atomIter;
63 >    AtomInfo *                    atomInfo;
64  
65 <    myAtoms = rb->getAtoms();    
66 <    
31 <    for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
32 <      internalVisit(*atomIter);
65 >    if (isIgnoreType(rb->getType())) {
66 >        internalVisit(rb);
67  
68 <  }
69 <  
68 >        myAtoms = rb->getAtoms();
69 >
70 >        for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
71 >            internalVisit(*atomIter);
72 >    }
73   }
74  
75 < bool IgnoreVisitor::isIgnoreType(const string& name){
76 <  return itList.find(name) != itList.end() ? true : false;
75 > bool IgnoreVisitor::isIgnoreType(const std::string&name) {
76 > return itList.find(name) != itList.end() ? true : false;
77   }
78  
79 < void IgnoreVisitor::internalVisit(StuntDouble* sd){
80 <  GenericData* data;
81 <  data = sd->getProperty("IGNORE");
82 <
83 <  //if this stuntdoulbe is already marked as ignore just skip it
84 <  if (data == NULL){
85 <    data = new GenericData;
86 <    data->setID("IGNORE");
87 <    sd->addProperty(data);
88 <  }
89 <    
79 > void IgnoreVisitor::internalVisit(StuntDouble *sd) {
80 >    info->getSelectionManager()->clearSelection(sd);
81 >    //GenericData *data;
82 >    //data = sd->getPropertyByName("IGNORE");
83 >    //
84 >    ////if this stuntdoulbe is already marked as ignore just skip it
85 >    //if (data == NULL) {
86 >    //    data = new GenericData;
87 >    //    data->setID("IGNORE");
88 >    //    sd->addProperty(data);
89 >    //}
90   }
91  
92 < const string IgnoreVisitor::toString(){
93 <  char buffer[65535];
94 <  string result;
95 <  set<string>::iterator i;
59 <  
60 <  sprintf(buffer ,"------------------------------------------------------------------\n");
61 <  result += buffer;
92 > const std::string IgnoreVisitor::toString() {
93 >    char                            buffer[65535];
94 >    std::string                     result;
95 >    std::set<std::string>::iterator i;
96  
97 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
98 <  result += buffer;
97 >    sprintf(buffer,
98 >            "------------------------------------------------------------------\n");
99 >    result += buffer;
100  
101 <  sprintf(buffer ,"Visitor Description: ignore  stuntdoubles\n");
102 <  result += buffer;
101 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
102 >    result += buffer;
103  
104 <  //print the ignore type list
105 <  sprintf(buffer , "Ignore type list contains below types:\n");
71 <  result += buffer;
104 >    sprintf(buffer, "Visitor Description: ignore  stuntdoubles\n");
105 >    result += buffer;
106  
107 <  for(i = itList.begin(); i != itList.end(); ++i){
108 <    sprintf(buffer ,"%s\t", i->c_str());
107 >    //print the ignore type list
108 >    sprintf(buffer, "Ignore type list contains below types:\n");
109      result += buffer;
110  
111 <  }
112 <  sprintf(buffer ,"\n");
113 <  result += buffer;
111 >    for( i = itList.begin(); i != itList.end(); ++i ) {
112 >        sprintf(buffer, "%s\t", i->c_str());
113 >        result += buffer;
114 >    }
115  
116 <  sprintf(buffer ,"------------------------------------------------------------------\n");
117 <  result += buffer;
116 >    sprintf(buffer, "\n");
117 >    result += buffer;
118  
119 <  return result;
119 >    sprintf(buffer,
120 >            "------------------------------------------------------------------\n");
121 >    result += buffer;
122 >
123 >    return result;
124   }
125  
126   //----------------------------------------------------------------------------//
127  
128 < void WrappingVisitor::visit(Atom* atom){
129 <  internalVisit(atom);
128 > void WrappingVisitor::visit(Atom *atom) {
129 > internalVisit(atom);
130   }
131 < void WrappingVisitor::visit(DirectionalAtom* datom){
132 <  internalVisit(datom);
131 >
132 > void WrappingVisitor::visit(DirectionalAtom *datom) {
133 > internalVisit(datom);
134   }
135  
136 < void WrappingVisitor::visit(RigidBody* rb){
137 <  internalVisit(rb);
136 > void WrappingVisitor::visit(RigidBody *rb) {
137 > internalVisit(rb);
138   }
139  
140 < void WrappingVisitor::internalVisit(StuntDouble* sd){
141 <  GenericData* data;
142 <  AtomData* atomData;
143 <  AtomInfo* atomInfo;
144 <  vector<AtomInfo*>::iterator i;
140 > void WrappingVisitor::internalVisit(StuntDouble *sd) {
141 >    GenericData *                     data;
142 >    AtomData *                        atomData;
143 >    AtomInfo *                        atomInfo;
144 >    std::vector<AtomInfo *>::iterator i;
145  
146 <  data = sd->getProperty("ATOMDATA");
107 <  if(data != NULL){
108 <    atomData = dynamic_cast<AtomData*>(data);  
109 <    if(atomData == NULL)
110 <      return;
111 <  }
112 <  else
113 <    return;
146 >    data = sd->getPropertyByName("ATOMDATA");
147  
148 <  for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i))
149 <    info->wrapVector(atomInfo->pos);
148 >    if (data != NULL) {
149 >        atomData = dynamic_cast<AtomData *>(data);
150  
151 <  
151 >        if (atomData == NULL)
152 >            return;
153 >    } else
154 >        return;
155 >
156 >    Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
157 >    
158 >    for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
159 >        currSnapshot->wrapVector(atomInfo->pos);
160 >    }
161   }
162  
163 < const string WrappingVisitor::toString(){
164 <  char buffer[65535];
165 <  string result;
124 <  
125 <  sprintf(buffer ,"------------------------------------------------------------------\n");
126 <  result += buffer;
163 > const std::string WrappingVisitor::toString() {
164 >    char        buffer[65535];
165 >    std::string result;
166  
167 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
168 <  result += buffer;
167 >    sprintf(buffer,
168 >            "------------------------------------------------------------------\n");
169 >    result += buffer;
170  
171 <  sprintf(buffer ,"Visitor Description: wrapping atoms back to periodic box\n");
172 <  result += buffer;
133 <
134 <  sprintf(buffer,"------------------------------------------------------------------\n");
135 <  result += buffer;
171 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
172 >    result += buffer;
173  
174 <  return result;
174 >    sprintf(buffer,
175 >            "Visitor Description: wrapping atoms back to periodic box\n");
176 >    result += buffer;
177 >
178 >    sprintf(buffer,
179 >            "------------------------------------------------------------------\n");
180 >    result += buffer;
181 >
182 >    return result;
183   }
184  
185   //----------------------------------------------------------------------------//
186  
187 < ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 opt) : BaseVisitor(){
188 <  this->info = info;
189 <  visitorName = "ReplicateVisitor";
190 <  this->replicateOpt = opt;
191 <  //generate the replicate directions
192 <  for(int i = 0; i <= replicateOpt[0]; i ++)
193 <    for(int j = 0; j <= replicateOpt[1]; j ++)
194 <      for(int k = 0; k <= replicateOpt[2]; k ++)
195 <        //skip original frame
196 <        if(i == 0 && j ==0 && k ==0)
197 <          continue;
198 <        else
199 <          dir.push_back(IntVec3(i, j, k));
200 <  
187 > ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
188 >    BaseVisitor() {
189 >    this->info = info;
190 >    visitorName = "ReplicateVisitor";
191 >    this->replicateOpt = opt;
192 >
193 >    //generate the replicate directions
194 >    for( int i = 0; i <= replicateOpt[0]; i++ ) {
195 >        for( int j = 0; j <= replicateOpt[1]; j++ ) {
196 >            for( int k = 0; k <= replicateOpt[2]; k++ ) {
197 >                //skip original frame
198 >                if (i == 0 && j == 0 && k == 0) {
199 >                    continue;
200 >                } else {
201 >                    dir.push_back(Vector3i(i, j, k));
202 >                }
203 >            }
204 >        }
205 >    }
206 >    
207   }
208 < void ReplicateVisitor::visit(Atom* atom){
209 <  internalVisit(atom);
208 >
209 > void ReplicateVisitor::visit(Atom *atom) {
210 > internalVisit(atom);
211   }
212 < void ReplicateVisitor::visit(DirectionalAtom* datom){
213 <  internalVisit(datom);
212 >
213 > void ReplicateVisitor::visit(DirectionalAtom *datom) {
214 > internalVisit(datom);
215   }
216  
217 < void ReplicateVisitor::visit(RigidBody* rb){
218 <  internalVisit(rb);
217 > void ReplicateVisitor::visit(RigidBody *rb) {
218 > internalVisit(rb);
219   }
220  
221 < void ReplicateVisitor::internalVisit(StuntDouble* sd){
222 <  GenericData* data;
223 <  AtomData* atomData;
171 <  AtomInfo* atomInfo;
172 <  double box[3][3];
173 <  vector<AtomInfo*> atomInfoList;
174 <  IntVec3 dir;
175 <  
176 <  //if there is not atom data, just skip it
177 <  data = sd->getProperty("ATOMDATA");
178 <  if(data != NULL){
179 <    atomData = dynamic_cast<AtomData*>(data);  
180 <    if(atomData == NULL)
181 <      return;
182 <  }
183 <  else
184 <    return;
221 > void ReplicateVisitor::internalVisit(StuntDouble *sd) {
222 >    GenericData *          data;
223 >    AtomData *             atomData;
224  
225 <  
226 <  info->getBoxM(box);
225 >    //if there is not atom data, just skip it
226 >    data = sd->getPropertyByName("ATOMDATA");
227  
228 <  atomInfoList = atomData->getData();
229 <  
191 <  replicate(atomInfoList, atomData, box);
228 >    if (data != NULL) {
229 >        atomData = dynamic_cast<AtomData *>(data);
230  
231 +        if (atomData == NULL) {
232 +            return;
233 +        }
234 +    } else {
235 +        return;
236 +    }
237 +
238 +    Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
239 +    Mat3x3d box = currSnapshot->getHmat();
240 +
241 +    std::vector<AtomInfo *> atomInfoList = atomData->getData();
242 +
243 +    replicate(atomInfoList, atomData, box);
244   }
245  
246 < void ReplicateVisitor::replicate(vector<AtomInfo*>& infoList, AtomData* data, double boxM[3][3]){
247 <  AtomInfo * newAtomInfo;
248 <  vector<IntVec3>::iterator dirIter;
249 <  vector<AtomInfo*>::iterator i;
199 <  
200 <  for(dirIter = dir.begin(); dirIter != dir.end(); ++dirIter){
201 <    for(i = infoList.begin(); i != infoList.end(); i++){
202 <      newAtomInfo = new AtomInfo;
203 <      *newAtomInfo = *(*i);    
246 > void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) {
247 >    AtomInfo* newAtomInfo;
248 >    std::vector<Vector3i>::iterator dirIter;
249 >    std::vector<AtomInfo *>::iterator i;
250  
251 <      for(int j = 0; j < 3; j++)
252 <        newAtomInfo->pos[j] +=   (*dirIter)[0] * boxM[j][0] + (*dirIter)[1]* boxM[j][1] + (*dirIter)[2] * boxM[j][2];
251 >    for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
252 >        for( i = infoList.begin(); i != infoList.end(); i++ ) {
253 >            newAtomInfo = new AtomInfo();
254 >            *newAtomInfo = *(*i);
255  
256 <      data->addAtomInfo(newAtomInfo);
257 <    }
258 <  }// end for(dirIter)  
256 >            for( int j = 0; j < 3; j++ )
257 >                newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2);
258 >
259 >            data->addAtomInfo(newAtomInfo);
260 >        }
261 >    } // end for(dirIter)  
262   }
263  
264 < const string ReplicateVisitor::toString(){
265 <  char buffer[65535];
266 <  string result;
267 <  set<string>::iterator i;
217 <  
218 <  sprintf(buffer ,"------------------------------------------------------------------\n");
219 <  result += buffer;
264 > const std::string ReplicateVisitor::toString() {
265 >    char                            buffer[65535];
266 >    std::string                     result;
267 >    std::set<std::string>::iterator i;
268  
269 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
270 <  result += buffer;
269 >    sprintf(buffer,
270 >            "------------------------------------------------------------------\n");
271 >    result += buffer;
272  
273 <  sprintf(buffer ,"Visitor Description: replicate the atoms in different direction\n");
274 <  result += buffer;
226 <  
227 <  //print the replicate direction
228 <  sprintf(buffer , "repeatX = %d:\n", replicateOpt[0]);
229 <  result += buffer;
273 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
274 >    result += buffer;
275  
276 <  sprintf(buffer , "repeatY = %d:\n", replicateOpt[1]);
277 <  result += buffer;
276 >    sprintf(buffer,
277 >            "Visitor Description: replicate the atoms in different direction\n");
278 >    result += buffer;
279  
280 <  sprintf(buffer , "repeatZ = %d:\n", replicateOpt[2]);
281 <  result += buffer;
280 >    //print the replicate direction
281 >    sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
282 >    result += buffer;
283  
284 +    sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
285 +    result += buffer;
286  
287 <  sprintf(buffer,"------------------------------------------------------------------\n");
288 <  result += buffer;
287 >    sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
288 >    result += buffer;
289  
290 <  return result;
290 >    sprintf(buffer,
291 >            "------------------------------------------------------------------\n");
292 >    result += buffer;
293 >
294 >    return result;
295   }
296  
297   //----------------------------------------------------------------------------//
298  
299 < XYZVisitor::XYZVisitor(SimInfo* info,  bool printDipole) : BaseVisitor(){
300 <  this->info = info;
301 <  visitorName = "XYZVisitor";
302 <  this->printDipole = printDipole;
299 > XYZVisitor::XYZVisitor(SimInfo *info, bool printDipole) :
300 >    BaseVisitor() {
301 >    this->info = info;
302 >    visitorName = "XYZVisitor";
303 >    this->printDipole = printDipole;
304   }
305  
306 < void XYZVisitor::visit(Atom* atom){
307 <  if(!isIgnore(atom))
308 <    internalVisit(atom);
306 > void XYZVisitor::visit(Atom *atom) {
307 >    if (isSelected(atom))
308 >        internalVisit(atom);
309   }
310  
311 < void XYZVisitor::visit(DirectionalAtom* datom){
312 <  if(!isIgnore(datom))
313 <    internalVisit(datom);
311 > void XYZVisitor::visit(DirectionalAtom *datom) {
312 >    if (isSelected(datom))
313 >        internalVisit(datom);
314   }
315  
316 < void XYZVisitor::visit(RigidBody* rb){
317 <  if(!isIgnore(rb))
318 <    internalVisit(rb);
316 > void XYZVisitor::visit(RigidBody *rb) {
317 >    if (isSelected(rb))
318 >        internalVisit(rb);
319 > }
320 >
321 > void XYZVisitor::internalVisit(StuntDouble *sd) {
322 >    GenericData *                     data;
323 >    AtomData *                        atomData;
324 >    AtomInfo *                        atomInfo;
325 >    std::vector<AtomInfo *>::iterator i;
326 >    char                              buffer[1024];
327 >
328 >    //if there is not atom data, just skip it
329 >    data = sd->getPropertyByName("ATOMDATA");
330  
331 < }
331 >    if (data != NULL) {
332 >        atomData = dynamic_cast<AtomData *>(data);
333  
334 < void XYZVisitor::internalVisit(StuntDouble* sd){
335 <  GenericData* data;
336 <  AtomData* atomData;
337 <  AtomInfo* atomInfo;
272 <  vector<AtomInfo*>::iterator i;
273 <  char buffer[1024];
274 <  
275 <  //if there is not atom data, just skip it
276 <  data = sd->getProperty("ATOMDATA");
277 <  if(data != NULL){
278 <    atomData = dynamic_cast<AtomData*>(data);  
279 <    if(atomData == NULL)
280 <      return;
281 <  }
282 <  else
283 <    return;
334 >        if (atomData == NULL)
335 >            return;
336 >    } else
337 >        return;
338  
339 <  for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){
339 >    for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
340 >        atomInfo = atomData->nextAtomInfo(i) ) {
341 >        if (printDipole)
342 >            sprintf(buffer,
343 >                    "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
344 >                    atomInfo->AtomType.c_str(),
345 >                    atomInfo->pos[0],
346 >                    atomInfo->pos[1],
347 >                    atomInfo->pos[2],
348 >                    atomInfo->dipole[0],
349 >                    atomInfo->dipole[1],
350 >                    atomInfo->dipole[2]); else
351 >            sprintf(buffer,                     "%s%15.8f%15.8f%15.8f",
352 >                    atomInfo->AtomType.c_str(), atomInfo->pos[0],
353 >                    atomInfo->pos[1],           atomInfo->pos[2]);
354  
355 <    if(printDipole)
356 <      sprintf(buffer, "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
289 <                  atomInfo->AtomType.c_str(),
290 <                  atomInfo->pos[0],
291 <                  atomInfo->pos[1],
292 <                  atomInfo->pos[2],
293 <                  atomInfo->dipole[0],
294 <                  atomInfo->dipole[1],
295 <                  atomInfo->dipole[2]);
296 <    else
297 <      sprintf(buffer, "%s%15.8f%15.8f%15.8f",
298 <                  atomInfo->AtomType.c_str(),
299 <                  atomInfo->pos[0],
300 <                  atomInfo->pos[1],
301 <                  atomInfo->pos[2]);  
302 <
303 <    frame.push_back(buffer);
304 <              
305 <  }
306 <
355 >        frame.push_back(buffer);
356 >    }
357   }
358  
359 < bool XYZVisitor::isIgnore(StuntDouble* sd){
360 <  GenericData* data;
311 <  
312 <  data = sd->getProperty("IGNORE");
313 <  return data ==NULL ? false : true;
359 > bool XYZVisitor::isSelected(StuntDouble *sd) {
360 >    return info->getSelectionManager()->isSelected(sd);
361   }
362  
363 < void XYZVisitor::writeFrame(ostream& outStream){
364 <  vector<string>::iterator i;
365 <  double box[3][3];
319 <  char buffer[1024];
363 > void XYZVisitor::writeFrame(std::ostream &outStream) {
364 >    std::vector<std::string>::iterator i;
365 >    char buffer[1024];
366  
367 <  if(frame.size() == 0)
368 <    cerr << "Current Frame does not contain any atoms" << endl;
367 >    if (frame.size() == 0)
368 >        std::cerr << "Current Frame does not contain any atoms" << std::endl;
369  
370 <  //total number of atoms  
371 <  outStream << frame.size() << endl;
370 >    //total number of atoms  
371 >    outStream << frame.size() << std::endl;
372  
373 <  //write comment line
374 <  info->getBoxM(box);
375 <  sprintf(buffer,"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
376 <              info->getTime(),
377 <              box[0][0], box[0][1], box[0][2],
378 <              box[1][0], box[1][1], box[1][2],
379 <              box[2][0], box[2][1], box[2][2]);
373 >    //write comment line
374 >    Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
375 >    Mat3x3d box = currSnapshot->getHmat();
376 >    
377 >    sprintf(buffer,
378 >            "%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
379 >            currSnapshot->getTime(),
380 >            box(0, 0), box(0, 1), box(0, 2),
381 >            box(1, 0), box(1, 1), box(1, 2),
382 >            box(2, 0), box(2, 1), box(2, 2));
383  
384 <  outStream << buffer << endl;  
384 >    outStream << buffer << std::endl;
385  
386 <  for(i = frame.begin(); i != frame.end(); ++i)
387 <    outStream << *i << endl;
386 >    for( i = frame.begin(); i != frame.end(); ++i )
387 >        outStream << *i << std::endl;
388   }
389  
390 < const string XYZVisitor::toString(){
391 <  char buffer[65535];
392 <  string result;
344 <  
345 <  sprintf(buffer ,"------------------------------------------------------------------\n");
346 <  result += buffer;
390 > const std::string XYZVisitor::toString() {
391 >    char        buffer[65535];
392 >    std::string result;
393  
394 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
395 <  result += buffer;
394 >    sprintf(buffer,
395 >            "------------------------------------------------------------------\n");
396 >    result += buffer;
397  
398 <  sprintf(buffer ,"Visitor Description: assemble the atom data and output xyz file\n");
399 <  result += buffer;
353 <
354 <  sprintf(buffer,"------------------------------------------------------------------\n");
355 <  result += buffer;
398 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
399 >    result += buffer;
400  
401 <  return result;
401 >    sprintf(buffer,
402 >            "Visitor Description: assemble the atom data and output xyz file\n");
403 >    result += buffer;
404 >
405 >    sprintf(buffer,
406 >            "------------------------------------------------------------------\n");
407 >    result += buffer;
408 >
409 >    return result;
410   }
411  
412   //----------------------------------------------------------------------------//
413  
414 < void PrepareVisitor::internalVisit(Atom * atom){
415 <  GenericData* data;
416 <  AtomData* atomData;
414 > void PrepareVisitor::internalVisit(Atom *atom) {
415 >    GenericData *data;
416 >    AtomData *   atomData;
417  
418 <  //if visited property is  existed, remove it
419 <  data = atom->getProperty("VISITED");
368 <  if(data != NULL){
369 <    atom->removeProperty("VISITED");  
370 <  }
418 >    //if visited property is  existed, remove it
419 >    data = atom->getPropertyByName("VISITED");
420  
421 <  //remove atomdata
422 <  data = atom->getProperty("ATOMDATA");
423 <  if(data != NULL){
375 <    atomData = dynamic_cast<AtomData*>(data);  
376 <    if(atomData != NULL)
377 <      atom->removeProperty("ATOMDATA");
378 <  }
379 <  
380 < }
421 >    if (data != NULL) {
422 >    atom->removeProperty("VISITED");
423 >    }
424  
425 < void PrepareVisitor::internalVisit(RigidBody * rb){
426 <  GenericData* data;
384 <  AtomData* atomData;
385 <  vector<Atom*> myAtoms;
386 <  vector<Atom*>::iterator atomIter;
387 <  
388 <  //if visited property is  existed, remove it
389 <  data = rb->getProperty("VISITED");
390 <  if(data != NULL){
391 <    rb->removeProperty("VISITED");  
392 <  }
425 >    //remove atomdata
426 >    data = atom->getPropertyByName("ATOMDATA");
427  
428 <  //remove atomdata
429 <  data = rb->getProperty("ATOMDATA");
396 <  if(data != NULL){
397 <    atomData = dynamic_cast<AtomData*>(data);  
398 <    if(atomData != NULL)
399 <      rb->removeProperty("ATOMDATA");
400 <  }
428 >    if (data != NULL) {
429 >        atomData = dynamic_cast<AtomData *>(data);
430  
431 <  myAtoms = rb->getAtoms();
432 <    
433 <  for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
405 <   internalVisit (*atomIter);  
431 >        if (atomData != NULL)
432 >            atom->removeProperty("ATOMDATA");
433 >    }
434   }
435  
436 < const string PrepareVisitor::toString(){
437 <  char buffer[65535];
438 <  string result;
439 <  
440 <  sprintf(buffer ,"------------------------------------------------------------------\n");
413 <  result += buffer;
436 > void PrepareVisitor::internalVisit(RigidBody *rb) {
437 >    GenericData* data;
438 >    AtomData* atomData;
439 >    std::vector<Atom *> myAtoms;
440 >    std::vector<Atom *>::iterator atomIter;
441  
442 <  sprintf(buffer ,"Visitor name: %s", visitorName.c_str());
443 <  result += buffer;
442 >    //if visited property is  existed, remove it
443 >    data = rb->getPropertyByName("VISITED");
444  
445 <  sprintf(buffer ,"Visitor Description: prepare for operation of other vistors\n");
446 <  result += buffer;
445 >    if (data != NULL) {
446 >    rb->removeProperty("VISITED");
447 >    }
448  
449 <  sprintf(buffer ,"------------------------------------------------------------------\n");
450 <  result += buffer;
449 >    //remove atomdata
450 >    data = rb->getPropertyByName("ATOMDATA");
451  
452 <  return result;
452 >    if (data != NULL) {
453 >        atomData = dynamic_cast<AtomData *>(data);
454 >
455 >        if (atomData != NULL)
456 >            rb->removeProperty("ATOMDATA");
457 >    }
458 >
459 >    myAtoms = rb->getAtoms();
460 >
461 >    for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
462 >        internalVisit(*atomIter);
463   }
464  
465 + const std::string PrepareVisitor::toString() {
466 +     char buffer[65535];
467 +     std::string result;
468 +
469 +     sprintf(buffer,
470 +             "------------------------------------------------------------------\n");
471 +     result += buffer;
472 +
473 +     sprintf(buffer, "Visitor name: %s", visitorName.c_str());
474 +     result += buffer;
475 +
476 +     sprintf(buffer,
477 +             "Visitor Description: prepare for operation of other vistors\n");
478 +     result += buffer;
479 +
480 +     sprintf(buffer,
481 +             "------------------------------------------------------------------\n");
482 +     result += buffer;
483 +
484 +     return result;
485 + }
486 +
487   //----------------------------------------------------------------------------//
488  
489 < WaterTypeVisitor:: WaterTypeVisitor(){
490 <  visitorName = "WaterTypeVisitor";
491 <  waterTypeList.insert("TIP3P_RB_0");
492 <  waterTypeList.insert("TIP4P_RB_0");
493 <  waterTypeList.insert("TIP5P_RB_0");
494 <  waterTypeList.insert("SPCE_RB_0");  
489 > WaterTypeVisitor::WaterTypeVisitor() {
490 >    visitorName = "WaterTypeVisitor";
491 >    waterTypeList.insert("TIP3P_RB_0");
492 >    waterTypeList.insert("TIP4P_RB_0");
493 >    waterTypeList.insert("TIP5P_RB_0");
494 >    waterTypeList.insert("SPCE_RB_0");
495   }
496  
497 + void WaterTypeVisitor::visit(RigidBody *rb) {
498 +    std::string rbName;
499 +    std::vector<Atom *> myAtoms;
500 +    std::vector<Atom *>::iterator atomIter;
501 +    GenericData* data;
502 +    AtomData* atomData;
503 +    AtomInfo* atomInfo;
504 +    std::vector<AtomInfo *>::iterator i;
505  
506 < void WaterTypeVisitor:: visit(RigidBody* rb){
439 <  string rbName;
440 <  vector<Atom*> myAtoms;
441 <  vector<Atom*>::iterator atomIter;
442 <  GenericData* data;
443 <  AtomData* atomData;
444 <  AtomInfo* atomInfo;
445 <  vector<AtomInfo*>::iterator i;
446 <  
447 <  rbName = rb->getType();
506 >    rbName = rb->getType();
507  
508 <  if(waterTypeList.find(rbName) != waterTypeList.end()){
508 >    if (waterTypeList.find(rbName) != waterTypeList.end()) {
509 >        myAtoms = rb->getAtoms();
510  
511 <    myAtoms = rb->getAtoms();    
512 <    for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter){
511 >        for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
512 >            ++atomIter ) {
513 >            data = (*atomIter)->getPropertyByName("ATOMDATA");
514  
515 <      data = (*atomIter)->getProperty("ATOMDATA");
516 <      if(data != NULL){
456 <        atomData = dynamic_cast<AtomData*>(data);  
457 <        if(atomData == NULL)
458 <          continue;
459 <      }
460 <      else
461 <        continue;
462 <      
463 <      for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){
464 <        replaceType(atomInfo->AtomType);
465 <      }//end for(atomInfo)
515 >            if (data != NULL) {
516 >                atomData = dynamic_cast<AtomData *>(data);
517  
518 <    }//end for(atomIter)
519 <      
520 <  }//end if (waterTypeList.find(rbName) != waterTypeList.end())
521 <  
518 >                if (atomData == NULL)
519 >                    continue;
520 >            } else
521 >                continue;
522 >
523 >            for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
524 >                atomInfo = atomData->nextAtomInfo(i) ) {
525 >            replaceType(atomInfo->AtomType);
526 >            } //end for(atomInfo)
527 >        }     //end for(atomIter)
528 >    }         //end if (waterTypeList.find(rbName) != waterTypeList.end())
529   }
530  
531 < void WaterTypeVisitor:: replaceType(string& atomType){
532 <  atomType = atomType.substr(0, atomType.find('_'));
531 > void WaterTypeVisitor::replaceType(std::string&atomType) {
532 > atomType = atomType.substr(0, atomType.find('_'));
533   }
534  
535 < const string WaterTypeVisitor:: toString(){
536 <  char buffer[65535];
537 <  string result;
480 <  
481 <  sprintf(buffer ,"------------------------------------------------------------------\n");
482 <  result += buffer;
535 > const std::string WaterTypeVisitor::toString() {
536 >    char buffer[65535];
537 >    std::string result;
538  
539 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
540 <  result += buffer;
539 >    sprintf(buffer,
540 >            "------------------------------------------------------------------\n");
541 >    result += buffer;
542  
543 <  sprintf(buffer ,"Visitor Description: Replace the atom type in water model\n");
544 <  result += buffer;
543 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
544 >    result += buffer;
545  
546 <  sprintf(buffer ,"------------------------------------------------------------------\n");
547 <  result += buffer;
546 >    sprintf(buffer,
547 >            "Visitor Description: Replace the atom type in water model\n");
548 >    result += buffer;
549  
550 <  return result;
550 >    sprintf(buffer,
551 >            "------------------------------------------------------------------\n");
552 >    result += buffer;
553 >
554 >    return result;
555   }
556  
557 <
497 < }//namespace oopse
557 > } //namespace oopse

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